.. code-block:: python

	#!/usr/bin/env python
	# -*- coding: utf-8 -*-
	
	from __future__ import print_function
	import pymzml
	import os
	
	
	def main():
	    """
	    Compare multiple spectra and return the cosine distance between them.
	    The returned value is between 0 and 1, a returned value of 1
	    represents highest similarity.
	
	    usage:
	
	        ./compare_spectra.py
	
	    """
	    example_file = os.path.join(
	        os.path.dirname(__file__),
	        os.pardir,
	        'tests',
	        'data',
	        'example.mzML'
	    )
	    print(
	        """
	            Comparing spectra
	        """
	    )
	    # print(example_file)
	    run = pymzml.run.Reader(example_file)
	    tmp = []
	    for spec in run:
	        if spec.ms_level == 1:
	            print(
	                "Parsing spectrum lvl 1 has id {0}".format(
	                    spec.ID
	                )
	            )
	            tmp.append( spec )
	            if len(tmp) >= 3:
	                break
	
	    print(
	        "Print total number of specs collected {0}".format(
	            len(tmp)
	        )
	    )
	    for compare_tuples in [ (0, 1), (0, 2), (1, 2) ]:
	        print(
	            "Cosine between spectra {0} & {1} is {2:1.4f}".format(
	                compare_tuples[0] + 1,
	                compare_tuples[1] + 1,
	                tmp[ compare_tuples[0] ].similarity_to( tmp[ compare_tuples[1] ] )
	            )
	        )
	
	    print(
	        "Cosine score between first spectrum against itself: {0:1.4f}".format(
	            tmp[0].similarity_to(tmp[0])
	        )
	    )
	
	
	if __name__ == '__main__':
	    main()
